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. 2024 Feb 16;111(3):456–472. doi: 10.1016/j.ajhg.2024.01.012

Table 2.

45 novel differentially methylated loci associated with TNEs in the discovery meta-analysis

 Discovery meta-analysis
 Validation meta-analysis
Probe_ID Chr Mapinfoa Gene Estimateb SE p value Estimateb SE p value
cg21901790 17 46599866 17q21.32 −0.0065 0.0009 4.22 × 10−13 −0.0048 0.0014 8.46 × 10−4
cg22548335 15 85473388 SLC28A1 −0.0067 0.0010 2.33 × 10−12 −0.0033 0.0013 0.01
cg10185953 5 139048784 CXXC5 −0.0072 0.0010 3.77 × 10−12 −0.0036 0.0018 0.04
cg03748458 8 14711248 MIR383;SGCZ −0.0104 0.0016 2.09 × 10−11 −0.0060 0.0030 0.04
cg09465516 2 54751985 SPTBN1 −0.0077 0.0012 3.14 × 10−11 −0.0027 0.0018 0.14
cg19931745 10 30984844 SVILP1 −0.0068 0.0011 1.31 × 10−10 −0.0022 0.0021 0.29
cg13218707 11 118900557 SLC37A4 −0.0096 0.0015 3.08 × 10−10 −0.0075 0.0028 7.52 × 10−3
cg16788982 20 33733327 EDEM2 −0.0097 0.0015 3.42 × 10−10 −0.0046 0.0020 0.02
cg18921991 5 173910163 LINC01411 −0.0051 0.0008 1.17 × 10−9 −0.0023 0.0012 0.06
cg23203766 15 79270157 RASGRF1 −0.0050 0.0008 1.22 × 10−9 −0.0033 0.0011 2.06 × 10−3
cg17408993 12 65110360 GNS 0.0063 0.0010 1.39 × 10−9 0.0073 0.0019 1.47 × 10−4
cg26540765 6 130065605 6q22.33 −0.0050 0.0008 1.45 × 10−9 −0.0018 0.0013 0.16
cg16485845 8 141802466 PTK2 −0.0035 0.0006 2.05 × 10−9 −0.0008 0.0009 0.38
cg15755028 11 64074198 ESRRA −0.0048 0.0008 2.33 × 10−9 −0.0022 0.0012 0.06
cg23690488 2 114299609 2q13 0.0034 0.0006 4.95 × 10−9 0.0009 0.0008 0.25
cg21594588 2 69869990 AAK1 0.0019 0.0003 5.88 × 10−9 0.0018 0.0008 0.03
cg07259245 10 101287322 LINC01475 −0.0062 0.0011 1.07 × 10−8 −0.0037 0.0018 0.04
cg03935228 7 104771546 SRPK2 −0.0035 0.0006 1.25 × 10−8 −0.0011 0.0011 0.32
cg01419727 5 131438977 5q31.1 −0.0051 0.0009 1.39 × 10−8 −0.0020 0.0014 0.17
cg07093667 10 23652849 10p12.2 −0.0040 0.0007 1.42 × 10−8 −0.0009 0.0012 0.47
cg22260008 7 27207318 HOXA10-AS; HOXA10-HOXA9 −0.0050 0.0009 1.45 × 10−8 −0.0014 0.0015 0.34
cg05889768 10 13143286 OPTN −0.0051 0.0009 1.70 × 10−8 −0.0040 0.0014 3.96 × 10−3
cg06446365 5 176729812 RAB24;PRELID1 −0.0057 0.0010 1.89 × 10−8 −0.0025 0.0019 0.18
cg17141212 7 99718026 TAF6;CNPY4 −0.0065 0.0012 2.26 × 10−8 −0.0043 0.0019 0.02
cg04233381 11 126243896 ST3GAL4 −0.0043 0.0008 2.61 × 10−8 −0.0011 0.0012 0.36
cg06538881 11 3011050 NAP1L4 −0.0087 0.0016 2.61 × 10−8 −0.0052 0.0029 0.07
cg02294028 7 114564373 MDFIC −0.0147 0.0026 2.64 × 10−8 0.0016 0.0056 0.77
cg01036611 17 2169272 SMG6 −0.0054 0.0010 2.90 × 10−8 −0.0013 0.0014 0.34
cg04878685 12 18584312 PIK3C2G −0.0045 0.0008 3.03 × 10−8 −0.0020 0.0014 0.17
cg21971539 14 39734390 CTAGE5 0.0043 0.0008 3.09 × 10−8 0.0035 0.0013 8.81 × 10−3
cg19716697 8 144449916 RHPN1-AS1;RHPN1 −0.0047 0.0009 3.62 × 10−8 −0.0017 0.0016 0.30
cg00172979 19 19549603 GATAD2A −0.0050 0.0009 3.98 × 10−8 0.0005 0.0014 0.71
cg08565919 16 4625419 C16orf96 0.0041 0.0008 4.05 × 10−8 −0.0001 0.0011 0.90
cg14691266 14 102277400 PPP2R5C −0.0067 0.0012 4.21 × 10−8 −0.0040 0.0025 0.12
cg10375645 16 20687193 ACSM1 0.0040 0.0007 4.26 × 10−8 0.0011 0.0012 0.35
cg26739807 17 49244797 NME2;NME1-NME2 −0.0076 0.0014 4.56 × 10−8 −0.0031 0.0020 0.11
cg10711136 11 86515053 PRSS23 −0.0065 0.0012 4.81 × 10−8 −0.0084 0.0020 1.81 × 10−5
cg25635022 3 170147199 CLDN11 −0.0048 0.0009 5.14 × 10−8 −0.0039 0.0013 2.81 × 10−3
cg07815896 15 40385132 BMF −0.0045 0.0008 5.45 × 10−8 0.0002 0.0015 0.91
cg14732445 14 61870472 PRKCH −0.0051 0.0009 5.47 × 10−8 −0.0004 0.0016 0.81
cg20404288 3 194023890 LINC00887 −0.0043 0.0008 5.92 × 10−8 −0.0016 0.0012 0.18
cg03026982 11 19953699 NAV2 −0.0057 0.0011 7.72 × 10−8 −0.0035 0.0017 0.03
cg23644132 11 3010640 NAP1L4 −0.0049 0.0009 8.40 × 10−8 −0.0028 0.0017 0.09
cg05422344 11 114033783 ZBTB16 −0.0062 0.0012 8.51 × 10−8 −0.0004 0.0019 0.82
cg08607482 15 75092823 CSK −0.0044 0.0008 8.62 × 10−8 −0.0029 0.0014 0.04

Discovery genome-wide significance threshold: p < 9 × 10−8.

Validation Bonferroni-corrected significance threshold: p < 1.23 × 10−4 (p = 0.05/408).

Results are ordered by statistical significance in the discovery meta-analysis.

a

Chromosomal coordinates based on GRCh37.

b

Parameter estimate representing the change in methylation β value per one log-unit increase in TNEs.